The PureCM Eclipse Plugin supports two forms of submit: 'Project Submit' and 'Workspace Submit'. 'Project Submit' will only allow you to submit files contained within the active Eclipse project. We imagine this will be the most common way of submitting your changes, so you are not confusing the changes you are making in one project with the changes you are making in another. 'Workspace Submit' will allow you to submit all changes within the PureCM workspace for which the active project belongs. This will allow you to perform cross-project submits if required.
To submit your changes to the server right-click the project in the 'Explorer' and select 'Team | Submit Project Changes to Server' or 'Team | Submit Workspace Changes to Server'.
This will launch the changeset dialog where you can view your changes and submit them to the server. The Changeset Dialog is described in the section called “Changeset Dialog”.